Extended shallow carbonate platform, pelagic, and drift deposits were drilled during International Ocean Discovery Program (IODP) Expedition 359 in the Inner Sea of the Maldives. These sediments yield rich and well-diversified benthic, planktonic foraminiferal and nannofossil assemblages spanning from the early Oligocene to the Recent. We present here the shore-based revised integrated biostratigraphy of these microfossil groups at IODP Hole 359-U1468A together with the paleobathymetric reconstruction. Our data suggests the presence of a late Oligocene carbonate platform, marked by the shallowest water depths of the entire sequence of around 80 m. This carbonate platform sequence occurred from around 29 Ma, the extrapolated minimum age estimate, at least up to 27.5 Ma and possibly up to 25.4 Ma. Up the sequence, similar carbonate production conditions occurred until 22.5 Ma across the Oligocene–Miocene transition, equated at 23.04 Ma, with increased water depths >120 m. Notably, in the time interval approximately from 24 to 21.5 Ma, orbitally induced sapropel layers indicate a change of open to restricted circulation. However, at around 22.5 Ma, pelagic deposition at a distal slope occurred with sedimentation rates of 3 cm/years. This initially occurred in water depths of >350 m but gradually reached deposition in water depths of >500 m, which persisted from 21.12 Ma until approximately the extrapolated age of 12.8 Ma. Sedimentation rates gradually increased to 10.5 cm/1000 years at around 450 m below sea floor, marking the initiation of the drift sequence as identified in seismic lines with an age estimate of 12.8 Ma. The initiation of the drift sequence is also marked by a drastic decrease in the preservation of benthic and planktonic foraminifera from good to very poor at around 12.8 Ma. The drift sequence essentially continued to the present day but was interrupted by two events: the deposition of distinct shallow water benthic shoals and a large hiatus. From 12.8 Ma, a shallowing upward bathymetry is suggested by the occurrence of shallow benthic foraminiferal assemblages that close to around 11.93 Ma reached a maximum water depth of 80 m. This shoal then prograded into the basin and persisted at least until 9.89 Ma. Basin conditions with water depths exceeding 500 m were re-established in the upper part of the sedimentary succession after a hiatus spanning approximately from 9.83 Ma to 2.39 Ma, implying that renewed open ocean conditions occurred in the Pliocene–Pleistocene part of the sedimentary record.